The dual role of fission yeast Tbc1/cofactor C orchestrates microtubule homeostasis in tubulin folding and acts as a GAP for GTPase Alp41/Arl2

Supplying the appropriate amount of correctly folded α/β-tubulin heterodimers is critical for microtubule dynamics. Formation of assembly-competent heterodimers is remarkably elaborate at the molecular level, in which the α- and β-tubulins are separately processed in a chaperone-dependent manner. This sequential step is performed by the tubulin-folding cofactor pathway, comprising a specific set of regulatory proteins: cofactors A–E. We identified the fission yeast cofactor: the orthologue of cofactor C, Tbc1. In addition to its roles in tubulin folding, Tbc1 acts as a GAP in regulating Alp41/Arl2, a highly conserved small GTPase. Of interest, the expression of GDP- or GTP-bound Alp41 showed the identical microtubule loss phenotype, suggesting that continuous cycling between these forms is important for its functions. In addition, we found that Alp41 interacts with Alp1^D, the orthologue of cofactor D, specifically when in the GDP-bound form. Intriguingly, Alp1^D colocalizes with microtubules when in excess, eventually leading to depolymerization, which is sequestered by co-overproducing GDP-bound Alp41. We present a model of the final stages of the tubulin cofactor pathway that includes a dual role for both Tbc1 and Alp1^D in opposing regulation of the microtubule.     

Synthesis of Aspartame Precursor Using Protease Suspended in Microaqueous Molten Amino Acids Mixture

Enzymatic synthesis of the aspartame precursor, N -(benzyloxycarbonyl)- l -aspartyl- l -phenylalanine methyl ester (Z-AspPheOMe) was performed with highly concentrated molten substrates. A mixture composed of molten N -(benzyloxycarbonyl)- l -aspartic acid (Z-Asp) and l -phenylalanine methyl ester (PheOMe) mixtures of 20 M could be prepared at 50°C. This Z-Asp/PheOMe mixture was applied to the enzymatic synthesis of Z-AspPheOMe using free thermolysin. Synthesis of Z-AspPheOMe was observed in the range of 100-150 &#119 l of NaOH solution (12.5 M) addition to a reaction mixture consisting of 1.0 mmol Z-Asp and 1.0 mmol PheOMe at 50°C. The enzymatic activity increased with increasing water addition, and reached a maximum at 100 &#119 l in addition to the reaction mixture of 1.0 mmol Z-Asp, 1.0 mmol PheOMe and 125 &#119 l of the NaOH solution. In this reaction system, the conversion at the reaction equilibrium was about 60%, the initial reaction rate calculated on the basis of the enzyme weight was 2.2 &#119 mol/g s, and the productivity calculated on the basis of the reaction mixture volume was 300 mol/m 3 h.     

In Vitro Experimental Study for the Determination of Cellular Axial Strain Threshold and Preferential Axial Strain from Cell Orientation Behavior in a Non-uniform Deformation Field

Cells within connective tissues are routinely subjected to a wide range of non-uniform mechanical loads that regulate many cell behaviors. In the present study, the relationship between cell orientation angle and strain value of the membrane was comprehensively investigated using an inhomogeneous strain field. Additionally, the cellular axial strain threshold, which corresponds to the launching of cell reorientation response, was elucidated. Human bone marrow mesenchymal stem cells were used for these experiments. In this study, an inhomogeneous strain distribution was easily created by removing one side holes of an elastic chamber in a commonly used uniaxial stretching device. The strains of 2D stretched membranes were quantified on a position-by-position basis using the digital image correlation method. The normal strain in the direction of stretch was changed continuously from 2.0 to 15.0 %. A 3D histogram of the cell frequency, which was correlated with the cell orientation angle and normal strain of the membrane, made it possible to determine the axial strain threshold accurately. The value of the axial strain threshold was 4.4 ± 0.3 %, which was reasonable compared with previous studies based on cyclic uniaxial stretch stimulation (homogeneous strain field). Additionally, preferential axial strain of cells, which was a cell property firstly introduced, was also achieved and the value was ?2.0 ± 0.1 %. This study is novel in three respects: (i) it precisely and easily determined the axial strain threshold of cells; (ii) it is the first to suggest preferential axial strain of cells; and (iii) it methodically investigated cell behavior in an inhomogeneous strain field.     

A spinach genome assembly with remarkable completeness,and its use for rapid identification of candidate genes for agronomic traits

Spinach (Spinacia oleracea) is grown as a nutritious leafy vegetable worldwide. To accelerate spinach breeding efficiency, a high-quality reference genome sequence with great completeness and continuity is needed as a basic infrastructure. Here, we used long-read and linked-read technologies to construct a de novo spinach genome assembly, designated SOL_r1.1, which was comprised of 287 scaffolds (total size: 935.7 Mb; N₅₀ = 11.3 Mb) with a low proportion of undetermined nucleotides (Ns = 0.34%) and with high gene completeness (BUSCO complete 96.9%). A genome-wide survey of resistance gene analogues identified 695 genes encoding nucleotide-binding site domains, receptor-like protein kinases, receptor-like proteins and transmembrane-coiled coil domains. Based on a high-density double-digest restriction-site associated DNA sequencing-based linkage map, the genome assembly was anchored to six pseudomolecules representing ∼73.5% of the whole genome assembly. In addition, we used SOL_r1.1 to identify quantitative trait loci for bolting timing and fruit/seed shape, which harbour biologically plausible candidate genes, such as homologues of the FLOWERING LOCUS T and EPIDERMAL PATTERNING FACTOR-LIKE genes. The new genome assembly, SOL_r1.1, will serve as a useful resource for identifying loci associated with important agronomic traits and for developing molecular markers for spinach breeding/selection programs.     

Role of individual dispersal in genetic resilience in fluctuating populations of the gray‐sided vole Myodes rufocanus

Population densities of the gray‐sided vole Myodes rufocanus fluctuate greatly within and across years in Japan. Here, to investigate the role of individual dispersal in maintaining population genetic diversity, we examined how genetic diversity varied during fluctuations in density by analyzing eight microsatellite loci in voles sampled three times per year for 5 years, using two fixed trapping grids (approximately 0.5 ha each). At each trapping session, all captured voles at each trapping grid were removed. The STRUCTURE program was used to analyze serially collected samples to examine how population crashes were related to temporal variability, based on local‐scale genetic compositions in each population. In total, 461 and 527 voles were captured at each trapping grid during this study. The number of voles captured during each trapping session (i.e., vole density) varied considerably at both grids. Although patterns in fluctuations were not synchronized between grids, the peak densities were similar. At both grids, the mean allele number recorded at each trapping session was strongly, positively, and nonlinearly correlated with density. STRUCTURE analyses revealed that the proportions of cluster compositions among individuals at each grid differed markedly before and after the crash phase, implying the long‐distance dispersal of voles from remote areas at periods of low density. The present results suggest that, in gray‐sided vole populations, genetic diversity varies with density largely at the local scale; in contrast, genetic variation in a metapopulation is well‐preserved at the regional scale due to the density‐dependent dispersal behaviors of individuals. By influencing the dispersal patterns of individuals, fluctuations in density affect metapopulation structure spatially and temporally, while the levels of genetic diversity are preserved in a metapopulation.     

Speciation along a latitudinal gradient: The origin of the Neotropical cycad sister pair Dioon sonorense–D. vovidesii (Zamiaceae)

Latitude is correlated with environmental components that determine the distribution of biodiversity. In combination with geographic factors, latitude‐associated environmental variables are expected to influence speciation, but empirical evidence on how those factors interplay is scarce. We evaluated the genetic and environmental variation among populations in the pair of sister species Dioon sonorense–D. vovidesii, two cycads distributed along a latitudinal environmental gradient in northwestern Mexico, to reveal their demographic histories and the environmental factors involved in their divergence. Using genome‐wide loci data, we determined the species delimitation, estimated the gene flow, and compared multiple demographic scenarios of divergence. Also, we estimated the variation of climatic variables among populations and used ecological niche models to test niche overlap between species. The effect of geographic and environmental variables on the genetic variation among populations was evaluated using linear models. Our results suggest the existence of a widespread ancestral population that split into the two species ~829 ky ago. The geographic delimitation along the environmental gradient occurs in the absence of major geographic barriers, near the 28th parallel north, where a zonation of environmental seasonality exists. The northern species, D. vovidesii, occurs in more seasonal environments but retains the same niche of the southern species, D. sonorense. The genetic variation throughout populations cannot be solely explained by stochastic processes; the latitudinal‐associated seasonality has been an additive factor that strengthened the species divergence. This study represents an example of how speciation can be achieved by the effect of the latitude‐associated factors on the genetic divergence among populations.     

Heading date 1 (Hd1), an ortholog of Arabidopsis CONSTANS, is a possible target of human selection during domestication to diversify flowering times of cultivated rice

During the domestication of rice (Oryza sativa L.), diversification of flowering time was important in expanding the areas of cultivation. Rice is a facultative short day (SD) plant and requires certain periods of dark to induce flowering. Heading date 1 (Hd1), a regulator of the florigen gene Hd3a, is one of the main factors used to generate diversity in flowering. Loss-of-function alleles of Hd1 are common in cultivated rice and cause the diversity of flowering time. However, it is unclear how these functional nucleotide polymorphisms of Hd1 accumulated in the course of evolution. Nucleotide polymorphisms within Hd1 and Hd3a were analyzed in 38 accessions of ancestral wild rice Oryza rufipogon and compared with those of cultivated rice. In contrast to cultivated rice, no nucleotide changes affecting Hd1 function were found in 38 accessions of wild rice ancestors. No functional changes were found in Hd3a in either cultivated or ancestral rice. A phylogenetic analysis indicated that evolution of the Hd1 alleles may have occurred independently in cultivars descended from various accessions of ancestral rice. The non-functional Hd1 alleles found in cultivated rice may be selected during domestication, because they were not found or very rare in wild ancestral rice. In contrast with Hd3a, which has been highly conserved, Hd1 may have undergone human selection to diversify the flowering times of rice during domestication or the early stage of the cultivation period.     

Interactions between normal and transformed epithelial cells: Their contributions to tumourigenesis

During the initial stages of carcinogenesis, neoplastic transformation occurs in single epithelial cells and the transformed cells proliferate while being surrounded by normal epithelia. In Drosophila, normal and transformed epithelial cells compete with each other for survival, a process called cell competition. However, it was not known whether comparable phenomena also occur in mammals. Recently, several reports have shown that the interaction between normal and transformed epithelial cells causes various phenomena in mammals. For example, with elaborate cell culture systems that express oncoproteins or knockdown tumour suppressor proteins in an inducible manner, certain types of transformed cells have been shown to be apically eliminated from normal epithelial layers in an apoptosis-dependent or -independent manner. During the process of apical extrusion, various signalling pathways are modulated in transformed cells located within the normal epithelium, indicating that the presence of surrounding normal epithelial cells affects the behaviour and fate of transformed cells. Recent studies in mice have also shown that normal and transformed cells can compete with each other for survival during several processes such as liver regeneration. In this review, we will introduce these recent publications on interactions between normal and transformed mammalian epithelial cells. Furthermore, we will discuss how these studies can potentially lead to identification of biomarkers for precancerous cells and to invention of novel types of cancer prevention and treatment.     

Expression and purification of human FROUNT, a common cytosolic regulator of CCR2 and CCR5

Chemokine receptors play pivotal roles for immune cell recruitment to inflammation sites, in response to chemokine gradients (chemotaxis). The mechanisms of chemokine signaling, especially the initiation of the intracellular signaling cascade, are not well understood. We previously identified a cytoplasmic protein FROUNT, which binds to the C-terminal regions of CCR2 and CCR5 to mediate chemokine signaling. Although large amounts of purified protein are required for detailed biochemical studies and drug screening, no method to produce recombinant FROUNT has been reported. In this study, we developed a method for the production of recombinant human FROUNT. Human FROUNT was successfully expressed in Escherichia coli, as a soluble protein fused to the folding chaperone Trigger Factor, with a cold shock expression system. The purified FROUNT protein displayed CCR2 binding ability without any additional components, as demonstrated by SPR measurements. A gel filtration analysis suggested that FROUNT exists in a homo-oligomeric state. This high-yield method is cost-effective for human FROUNT production. It should be a powerful tool for further biochemical and structural studies to elucidate GPCR regulation and chemokine signaling, and also will contribute to drug development.